rs156823

Positions:

• chr5-54043757-A-G
• chr5-54043757-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_019087.3(ARL15):​c.462+69445T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 151,878 control chromosomes in the GnomAD database, including 11,288 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.35 (11288 hom., cov: 31)
• Consequence: ARL15 NM_019087.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.623

Genes affected

ARL15 (HGNC:25945): (ADP ribosylation factor like GTPase 15) Predicted to enable GTP binding activity and GTPase activity. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARL15	NM_019087.3	c.462+69445T>C		intron_variant		ENST00000504924.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARL15	ENST00000504924.6	c.462+69445T>C		intron_variant		1	NM_019087.3	P1
ARL15	ENST00000502271.5	c.-76+69445T>C		intron_variant		1
ARL15	ENST00000507646.2	c.462+69445T>C		intron_variant		5
ARL15	ENST00000510591.6	n.535+69445T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52788 AN: 151760 Hom.: 11288 Cov.: 31

Gnomad AFR AF: 0.0877

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.358

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.348 AC: 52794 AN: 151878 Hom.: 11288 Cov.: 31 AF XY: 0.351 AC XY: 26081 AN XY: 74234

Gnomad4 AFR AF: 0.0875

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.492

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.445

Gnomad4 OTH AF: 0.354

Alfa AF: 0.405 Hom.: 2389

Bravo AF: 0.342

Asia WGS AF: 0.331 AC: 1152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.5
DANN	Benign	0.70
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs156823; hg19: chr5-53339587;